Starting phenix.real_space_refine on Sun Sep 29 20:55:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfy_12306/09_2024/7nfy_12306_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfy_12306/09_2024/7nfy_12306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfy_12306/09_2024/7nfy_12306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfy_12306/09_2024/7nfy_12306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfy_12306/09_2024/7nfy_12306_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfy_12306/09_2024/7nfy_12306_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 167 5.16 5 C 23514 2.51 5 N 6450 2.21 5 O 7006 1.98 5 H 37485 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 183 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74644 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 12392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12392 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "B" Number of atoms: 12369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12369 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "C" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "D" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "E" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "F" Number of atoms: 12394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12394 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "G" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 26.83, per 1000 atoms: 0.36 Number of scatterers: 74644 At special positions: 0 Unit cell: (141.772, 134.366, 230.644, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 167 16.00 P 17 15.00 Mg 5 11.99 O 7006 8.00 N 6450 7.00 C 23514 6.00 H 37485 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.59 Conformation dependent library (CDL) restraints added in 4.5 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8784 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 47 sheets defined 51.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 147 through 156 removed outlier: 4.089A pdb=" N GLU A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 290 through 307 removed outlier: 3.535A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.706A pdb=" N GLN A 322 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 323 " --> pdb=" O ALA A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 323' Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.670A pdb=" N LEU A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 354 through 407 removed outlier: 3.687A pdb=" N LEU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 427 removed outlier: 3.895A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.602A pdb=" N ILE A 468 " --> pdb=" O TRP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.997A pdb=" N ALA A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 Processing helix chain 'A' and resid 528 through 541 removed outlier: 4.235A pdb=" N ALA A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.681A pdb=" N GLN A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 Processing helix chain 'A' and resid 602 through 612 removed outlier: 4.090A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 removed outlier: 3.548A pdb=" N GLN A 677 " --> pdb=" O TYR A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 738 through 746 removed outlier: 4.118A pdb=" N GLN A 743 " --> pdb=" O PRO A 739 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASP A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 829 removed outlier: 3.656A pdb=" N GLU A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 838 removed outlier: 4.295A pdb=" N SER A 838 " --> pdb=" O LEU A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Proline residue: A 854 - end of helix Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 906 removed outlier: 3.791A pdb=" N LYS A 898 " --> pdb=" O GLY A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 924 through 929 removed outlier: 4.122A pdb=" N GLU A 929 " --> pdb=" O PHE A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 947 removed outlier: 3.535A pdb=" N PHE A 943 " --> pdb=" O TYR A 939 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 158 removed outlier: 3.693A pdb=" N GLU B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 292 through 307 removed outlier: 4.312A pdb=" N LYS B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 327 through 338 removed outlier: 3.784A pdb=" N LEU B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 354 through 389 Processing helix chain 'B' and resid 391 through 404 removed outlier: 3.728A pdb=" N LEU B 395 " --> pdb=" O HIS B 391 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.502A pdb=" N ILE B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 removed outlier: 3.887A pdb=" N ASP B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP B 439 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 466 removed outlier: 3.560A pdb=" N ASN B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.595A pdb=" N ALA B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 486 " --> pdb=" O ARG B 482 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 511 Processing helix chain 'B' and resid 528 through 541 removed outlier: 4.369A pdb=" N ALA B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 580 removed outlier: 3.502A pdb=" N GLN B 575 " --> pdb=" O GLY B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.992A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.925A pdb=" N ALA B 617 " --> pdb=" O GLU B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 4.110A pdb=" N MET B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 673 removed outlier: 3.574A pdb=" N ARG B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 683 removed outlier: 3.574A pdb=" N LEU B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 703 removed outlier: 3.531A pdb=" N ILE B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 729 removed outlier: 3.966A pdb=" N LEU B 720 " --> pdb=" O VAL B 716 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 723 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 729 " --> pdb=" O TYR B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 746 removed outlier: 3.830A pdb=" N LEU B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN B 743 " --> pdb=" O PRO B 739 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ASP B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 829 removed outlier: 3.817A pdb=" N GLU B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Proline residue: B 854 - end of helix Processing helix chain 'B' and resid 856 through 870 Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.645A pdb=" N ILE B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 922 removed outlier: 3.756A pdb=" N TYR B 921 " --> pdb=" O LYS B 917 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 917 through 922' Processing helix chain 'B' and resid 924 through 929 Processing helix chain 'B' and resid 938 through 947 Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.838A pdb=" N GLU C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.632A pdb=" N VAL C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 307 removed outlier: 3.717A pdb=" N GLU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 Processing helix chain 'C' and resid 319 through 323 removed outlier: 3.823A pdb=" N ARG C 323 " --> pdb=" O ALA C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 338 removed outlier: 3.673A pdb=" N LEU C 338 " --> pdb=" O MET C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 354 through 408 removed outlier: 3.699A pdb=" N LYS C 393 " --> pdb=" O GLN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 426 removed outlier: 3.525A pdb=" N LYS C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 448 removed outlier: 3.771A pdb=" N ASP C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.717A pdb=" N VAL C 486 " --> pdb=" O ARG C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 511 removed outlier: 3.729A pdb=" N LEU C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 541 removed outlier: 4.328A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 559 Processing helix chain 'C' and resid 571 through 580 removed outlier: 3.510A pdb=" N LYS C 579 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR C 580 " --> pdb=" O CYS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 602 through 612 removed outlier: 3.972A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.643A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 673 removed outlier: 4.579A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 672 " --> pdb=" O ALA C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 686 through 690 removed outlier: 3.704A pdb=" N ALA C 689 " --> pdb=" O GLU C 686 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS C 690 " --> pdb=" O SER C 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 686 through 690' Processing helix chain 'C' and resid 692 through 704 removed outlier: 4.064A pdb=" N LEU C 696 " --> pdb=" O SER C 692 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 697 " --> pdb=" O SER C 693 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 698 " --> pdb=" O ASP C 694 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS C 704 " --> pdb=" O ILE C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 729 removed outlier: 3.532A pdb=" N SER C 723 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 726 " --> pdb=" O LYS C 722 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 727 " --> pdb=" O SER C 723 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 729 " --> pdb=" O TYR C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 740 No H-bonds generated for 'chain 'C' and resid 738 through 740' Processing helix chain 'C' and resid 741 through 746 removed outlier: 3.561A pdb=" N PHE C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 829 removed outlier: 4.022A pdb=" N MET C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 removed outlier: 4.268A pdb=" N SER C 855 " --> pdb=" O LYS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 870 removed outlier: 3.710A pdb=" N VAL C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.628A pdb=" N LYS C 898 " --> pdb=" O GLY C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 915 No H-bonds generated for 'chain 'C' and resid 913 through 915' Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 939 through 947 removed outlier: 3.689A pdb=" N PHE C 943 " --> pdb=" O TYR C 939 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 156 removed outlier: 3.508A pdb=" N GLU D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 181 Processing helix chain 'D' and resid 290 through 307 removed outlier: 4.001A pdb=" N ALA D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 318 Processing helix chain 'D' and resid 319 through 323 removed outlier: 3.938A pdb=" N ARG D 323 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 338 removed outlier: 3.923A pdb=" N LEU D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 352 removed outlier: 3.616A pdb=" N GLU D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 389 Processing helix chain 'D' and resid 391 through 409 removed outlier: 3.780A pdb=" N LEU D 395 " --> pdb=" O HIS D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 426 removed outlier: 3.564A pdb=" N GLU D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 448 removed outlier: 4.008A pdb=" N ASP D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP D 439 " --> pdb=" O MET D 435 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU D 441 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 447 " --> pdb=" O SER D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 468 removed outlier: 3.917A pdb=" N ILE D 468 " --> pdb=" O TRP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 489 removed outlier: 3.845A pdb=" N ALA D 483 " --> pdb=" O ASP D 479 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 485 " --> pdb=" O ALA D 481 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 486 " --> pdb=" O ARG D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.561A pdb=" N LYS D 498 " --> pdb=" O MET D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 541 removed outlier: 4.010A pdb=" N ALA D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER D 535 " --> pdb=" O SER D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 560 removed outlier: 4.027A pdb=" N ILE D 558 " --> pdb=" O ASP D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 581 removed outlier: 3.760A pdb=" N GLN D 575 " --> pdb=" O GLY D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 595 Processing helix chain 'D' and resid 602 through 612 removed outlier: 3.901A pdb=" N ALA D 606 " --> pdb=" O ASP D 602 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 619 removed outlier: 3.668A pdb=" N ALA D 617 " --> pdb=" O GLU D 614 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN D 618 " --> pdb=" O GLN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.857A pdb=" N ARG D 652 " --> pdb=" O PRO D 648 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 671 removed outlier: 4.158A pdb=" N LEU D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 682 Processing helix chain 'D' and resid 692 through 703 removed outlier: 3.787A pdb=" N LEU D 696 " --> pdb=" O SER D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 729 removed outlier: 3.561A pdb=" N GLU D 717 " --> pdb=" O GLN D 713 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER D 729 " --> pdb=" O TYR D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 747 removed outlier: 4.359A pdb=" N GLN D 743 " --> pdb=" O PRO D 739 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP D 744 " --> pdb=" O GLU D 740 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE D 745 " --> pdb=" O ASN D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 829 removed outlier: 3.706A pdb=" N MET D 826 " --> pdb=" O ARG D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 855 Proline residue: D 854 - end of helix Processing helix chain 'D' and resid 856 through 870 removed outlier: 3.798A pdb=" N ILE D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 861 " --> pdb=" O GLY D 857 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR D 862 " --> pdb=" O CYS D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 905 removed outlier: 3.691A pdb=" N LYS D 898 " --> pdb=" O GLY D 894 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 900 " --> pdb=" O LYS D 896 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 905 " --> pdb=" O ALA D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 917 Processing helix chain 'D' and resid 918 through 923 Processing helix chain 'D' and resid 924 through 929 Processing helix chain 'D' and resid 938 through 947 removed outlier: 4.277A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 removed outlier: 3.533A pdb=" N GLU E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 Processing helix chain 'E' and resid 290 through 307 removed outlier: 3.559A pdb=" N ALA E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 318 Processing helix chain 'E' and resid 319 through 323 removed outlier: 3.530A pdb=" N GLN E 322 " --> pdb=" O GLN E 319 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG E 323 " --> pdb=" O ALA E 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 319 through 323' Processing helix chain 'E' and resid 327 through 338 removed outlier: 3.677A pdb=" N LEU E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 352 Processing helix chain 'E' and resid 354 through 404 removed outlier: 3.965A pdb=" N LEU E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 426 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.692A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY E 446 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU E 447 " --> pdb=" O SER E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 467 Processing helix chain 'E' and resid 479 through 491 removed outlier: 3.545A pdb=" N ALA E 485 " --> pdb=" O ALA E 481 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS E 491 " --> pdb=" O LEU E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 509 Processing helix chain 'E' and resid 528 through 541 removed outlier: 3.588A pdb=" N ILE E 532 " --> pdb=" O GLY E 528 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG E 534 " --> pdb=" O THR E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 571 through 580 removed outlier: 4.045A pdb=" N GLN E 575 " --> pdb=" O GLY E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 612 removed outlier: 4.113A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU E 611 " --> pdb=" O LEU E 607 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 612 " --> pdb=" O LEU E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 617 Processing helix chain 'E' and resid 646 through 653 removed outlier: 4.008A pdb=" N MET E 653 " --> pdb=" O LEU E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 671 Processing helix chain 'E' and resid 673 through 683 removed outlier: 3.570A pdb=" N ALA E 680 " --> pdb=" O PRO E 676 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU E 681 " --> pdb=" O GLN E 677 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 702 removed outlier: 3.949A pdb=" N LEU E 696 " --> pdb=" O SER E 692 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR E 697 " --> pdb=" O SER E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 729 removed outlier: 4.003A pdb=" N VAL E 719 " --> pdb=" O GLN E 715 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS E 726 " --> pdb=" O LYS E 722 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE E 727 " --> pdb=" O SER E 723 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 728 " --> pdb=" O ALA E 724 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER E 729 " --> pdb=" O TYR E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 747 Processing helix chain 'E' and resid 807 through 829 removed outlier: 3.631A pdb=" N MET E 826 " --> pdb=" O ARG E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 852 through 855 Processing helix chain 'E' and resid 856 through 870 removed outlier: 3.570A pdb=" N ILE E 860 " --> pdb=" O ALA E 856 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E 862 " --> pdb=" O CYS E 858 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU E 867 " --> pdb=" O ALA E 863 " (cutoff:3.500A) Processing helix chain 'E' and resid 894 through 905 Processing helix chain 'E' and resid 916 through 921 removed outlier: 3.868A pdb=" N PHE E 920 " --> pdb=" O ASN E 916 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR E 921 " --> pdb=" O LYS E 917 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 916 through 921' Processing helix chain 'E' and resid 924 through 929 Processing helix chain 'E' and resid 938 through 947 removed outlier: 4.240A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP E 944 " --> pdb=" O ARG E 940 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 174 through 181 Processing helix chain 'F' and resid 288 through 290 No H-bonds generated for 'chain 'F' and resid 288 through 290' Processing helix chain 'F' and resid 291 through 307 removed outlier: 4.449A pdb=" N GLU F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 Processing helix chain 'F' and resid 319 through 323 Processing helix chain 'F' and resid 327 through 338 removed outlier: 3.910A pdb=" N LEU F 331 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 352 removed outlier: 3.651A pdb=" N GLU F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 389 Processing helix chain 'F' and resid 391 through 405 removed outlier: 3.973A pdb=" N LEU F 395 " --> pdb=" O HIS F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 427 removed outlier: 3.955A pdb=" N ASP F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE F 417 " --> pdb=" O ASP F 413 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 448 removed outlier: 3.864A pdb=" N MET F 435 " --> pdb=" O PRO F 431 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP F 436 " --> pdb=" O LYS F 432 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU F 448 " --> pdb=" O LYS F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 468 removed outlier: 3.755A pdb=" N LEU F 465 " --> pdb=" O TYR F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 490 removed outlier: 3.762A pdb=" N VAL F 486 " --> pdb=" O ARG F 482 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU F 487 " --> pdb=" O ALA F 483 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 489 " --> pdb=" O ALA F 485 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP F 490 " --> pdb=" O VAL F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 511 removed outlier: 3.676A pdb=" N LEU F 502 " --> pdb=" O LYS F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 541 removed outlier: 3.748A pdb=" N ARG F 534 " --> pdb=" O THR F 530 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER F 535 " --> pdb=" O SER F 531 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG F 538 " --> pdb=" O ARG F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 571 through 580 removed outlier: 4.065A pdb=" N GLN F 575 " --> pdb=" O GLY F 571 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS F 576 " --> pdb=" O LYS F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 595 removed outlier: 4.218A pdb=" N LYS F 594 " --> pdb=" O GLU F 591 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE F 595 " --> pdb=" O VAL F 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 591 through 595' Processing helix chain 'F' and resid 603 through 612 removed outlier: 3.653A pdb=" N LEU F 607 " --> pdb=" O PRO F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 removed outlier: 4.030A pdb=" N ASN F 618 " --> pdb=" O GLN F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 651 Processing helix chain 'F' and resid 662 through 671 removed outlier: 4.053A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE F 669 " --> pdb=" O GLU F 665 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA F 670 " --> pdb=" O LYS F 666 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 682 removed outlier: 3.516A pdb=" N ALA F 680 " --> pdb=" O PRO F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 692 through 704 removed outlier: 3.867A pdb=" N CYS F 704 " --> pdb=" O ILE F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 729 removed outlier: 3.522A pdb=" N GLN F 715 " --> pdb=" O ASN F 711 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER F 729 " --> pdb=" O TYR F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 747 removed outlier: 4.045A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 746 " --> pdb=" O LEU F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 removed outlier: 3.697A pdb=" N SER F 813 " --> pdb=" O VAL F 809 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 815 " --> pdb=" O LYS F 811 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET F 826 " --> pdb=" O ARG F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 849 through 855 Proline residue: F 854 - end of helix Processing helix chain 'F' and resid 856 through 870 removed outlier: 3.859A pdb=" N ILE F 860 " --> pdb=" O ALA F 856 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU F 865 " --> pdb=" O VAL F 861 " (cutoff:3.500A) Processing helix chain 'F' and resid 894 through 904 removed outlier: 3.664A pdb=" N ARG F 904 " --> pdb=" O ILE F 900 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 923 removed outlier: 3.702A pdb=" N PHE F 920 " --> pdb=" O ASN F 916 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU F 923 " --> pdb=" O ASP F 919 " (cutoff:3.500A) Processing helix chain 'F' and resid 924 through 929 removed outlier: 4.013A pdb=" N THR F 928 " --> pdb=" O ALA F 924 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU F 929 " --> pdb=" O ALA F 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 924 through 929' Processing helix chain 'F' and resid 938 through 941 Processing helix chain 'F' and resid 942 through 947 removed outlier: 3.841A pdb=" N PHE F 947 " --> pdb=" O PHE F 943 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 164 Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 547 Processing sheet with id=AA5, first strand: chain 'A' and resid 689 through 690 removed outlier: 4.041A pdb=" N LYS A 690 " --> pdb=" O VAL A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 764 through 769 removed outlier: 3.870A pdb=" N GLU A 801 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 842 " --> pdb=" O GLU A 801 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 911 through 913 Processing sheet with id=AA8, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AA9, first strand: chain 'B' and resid 167 through 169 removed outlier: 4.887A pdb=" N LEU B 168 " --> pdb=" O TYR B 186 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.660A pdb=" N ALA B 639 " --> pdb=" O PHE B 521 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 547 through 548 removed outlier: 7.598A pdb=" N PHE B 547 " --> pdb=" O ASP B 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 689 through 690 removed outlier: 4.224A pdb=" N LYS B 690 " --> pdb=" O VAL B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 765 through 769 removed outlier: 3.654A pdb=" N VAL B 765 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 780 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 769 " --> pdb=" O SER B 776 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB6, first strand: chain 'C' and resid 163 through 164 removed outlier: 5.063A pdb=" N LEU C 168 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 163 through 164 Processing sheet with id=AB8, first strand: chain 'C' and resid 520 through 521 Processing sheet with id=AB9, first strand: chain 'C' and resid 544 through 548 removed outlier: 3.518A pdb=" N PHE C 547 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C 590 " --> pdb=" O PHE C 547 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 767 through 769 Processing sheet with id=AC2, first strand: chain 'C' and resid 781 through 784 removed outlier: 5.434A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 882 through 883 removed outlier: 3.501A pdb=" N GLU C 882 " --> pdb=" O LEU C 890 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AC5, first strand: chain 'D' and resid 163 through 164 removed outlier: 4.838A pdb=" N LEU D 168 " --> pdb=" O TYR D 186 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 163 through 164 Processing sheet with id=AC7, first strand: chain 'D' and resid 520 through 521 Processing sheet with id=AC8, first strand: chain 'D' and resid 544 through 548 removed outlier: 3.619A pdb=" N PHE D 545 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 689 through 690 removed outlier: 3.991A pdb=" N LYS D 690 " --> pdb=" O VAL D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 764 through 766 removed outlier: 5.942A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AD3, first strand: chain 'E' and resid 163 through 164 removed outlier: 5.168A pdb=" N LEU E 168 " --> pdb=" O TYR E 186 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 163 through 164 Processing sheet with id=AD5, first strand: chain 'E' and resid 638 through 639 removed outlier: 6.489A pdb=" N PHE E 521 " --> pdb=" O ALA E 639 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 544 through 548 removed outlier: 3.518A pdb=" N PHE E 545 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP E 590 " --> pdb=" O PHE E 547 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 619 through 620 removed outlier: 3.616A pdb=" N PHE E 619 " --> pdb=" O VAL E 628 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 689 through 690 removed outlier: 3.778A pdb=" N LYS E 690 " --> pdb=" O VAL E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 767 through 770 Processing sheet with id=AE1, first strand: chain 'E' and resid 781 through 784 removed outlier: 3.645A pdb=" N GLU E 781 " --> pdb=" O HIS E 843 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 882 through 883 removed outlier: 4.140A pdb=" N GLU E 882 " --> pdb=" O LEU E 890 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 911 through 913 removed outlier: 6.301A pdb=" N LEU E 912 " --> pdb=" O VAL E 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AE5, first strand: chain 'F' and resid 164 through 169 removed outlier: 6.738A pdb=" N VAL F 164 " --> pdb=" O THR F 190 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR F 190 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL F 166 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR F 188 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU F 168 " --> pdb=" O TYR F 186 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 521 through 522 Processing sheet with id=AE7, first strand: chain 'F' and resid 544 through 548 removed outlier: 3.615A pdb=" N PHE F 545 " --> pdb=" O LEU F 586 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP F 590 " --> pdb=" O PHE F 547 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 689 through 691 removed outlier: 7.175A pdb=" N LYS F 690 " --> pdb=" O VAL F 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'F' and resid 764 through 766 removed outlier: 3.556A pdb=" N GLU F 781 " --> pdb=" O HIS F 843 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 769 through 770 Processing sheet with id=AF2, first strand: chain 'F' and resid 909 through 913 1526 hydrogen bonds defined for protein. 4362 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.53 Time building geometry restraints manager: 18.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.03: 37443 1.03 - 1.25: 6383 1.25 - 1.48: 14743 1.48 - 1.71: 16406 1.71 - 1.94: 287 Bond restraints: 75262 Sorted by residual: bond pdb=" NE2 GLN C 389 " pdb="HE22 GLN C 389 " ideal model delta sigma weight residual 0.860 0.800 0.060 2.00e-02 2.50e+03 9.08e+00 bond pdb=" CD1 TYR D 492 " pdb=" CE1 TYR D 492 " ideal model delta sigma weight residual 1.382 1.292 0.090 3.00e-02 1.11e+03 8.98e+00 bond pdb=" CB TRP D 464 " pdb=" CG TRP D 464 " ideal model delta sigma weight residual 1.498 1.406 0.092 3.10e-02 1.04e+03 8.86e+00 bond pdb=" C LYS F 290 " pdb=" N ALA F 291 " ideal model delta sigma weight residual 1.335 1.373 -0.038 1.32e-02 5.74e+03 8.20e+00 bond pdb=" CB GLU E 882 " pdb=" CG GLU E 882 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 7.99e+00 ... (remaining 75257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.00: 136482 7.00 - 14.00: 106 14.00 - 21.00: 10 21.00 - 28.00: 17 28.00 - 35.00: 10 Bond angle restraints: 136625 Sorted by residual: angle pdb=" HE1 MET E 209 " pdb=" CE MET E 209 " pdb=" HE2 MET E 209 " ideal model delta sigma weight residual 110.00 75.00 35.00 3.00e+00 1.11e-01 1.36e+02 angle pdb=" SD MET E 209 " pdb=" CE MET E 209 " pdb=" HE2 MET E 209 " ideal model delta sigma weight residual 109.00 74.42 34.58 3.00e+00 1.11e-01 1.33e+02 angle pdb="HG11 VAL B 753 " pdb=" CG1 VAL B 753 " pdb="HG12 VAL B 753 " ideal model delta sigma weight residual 110.00 75.61 34.39 3.00e+00 1.11e-01 1.31e+02 angle pdb="HG11 VAL C 753 " pdb=" CG1 VAL C 753 " pdb="HG12 VAL C 753 " ideal model delta sigma weight residual 110.00 75.66 34.34 3.00e+00 1.11e-01 1.31e+02 angle pdb="HG11 VAL C 753 " pdb=" CG1 VAL C 753 " pdb="HG13 VAL C 753 " ideal model delta sigma weight residual 110.00 77.53 32.47 3.00e+00 1.11e-01 1.17e+02 ... (remaining 136620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.97: 32799 21.97 - 43.94: 1721 43.94 - 65.92: 387 65.92 - 87.89: 39 87.89 - 109.86: 11 Dihedral angle restraints: 34957 sinusoidal: 19646 harmonic: 15311 Sorted by residual: dihedral pdb=" C GLU B 288 " pdb=" N GLU B 288 " pdb=" CA GLU B 288 " pdb=" CB GLU B 288 " ideal model delta harmonic sigma weight residual -122.60 -107.39 -15.21 0 2.50e+00 1.60e-01 3.70e+01 dihedral pdb=" O1B ADP E1001 " pdb=" O3A ADP E1001 " pdb=" PB ADP E1001 " pdb=" PA ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 49.86 -109.86 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" N GLU B 288 " pdb=" C GLU B 288 " pdb=" CA GLU B 288 " pdb=" CB GLU B 288 " ideal model delta harmonic sigma weight residual 122.80 110.12 12.68 0 2.50e+00 1.60e-01 2.57e+01 ... (remaining 34954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.357: 5862 0.357 - 0.714: 2 0.714 - 1.071: 0 1.071 - 1.428: 0 1.428 - 1.785: 2 Chirality restraints: 5866 Sorted by residual: chirality pdb=" CG LEU D 425 " pdb=" CB LEU D 425 " pdb=" CD1 LEU D 425 " pdb=" CD2 LEU D 425 " both_signs ideal model delta sigma weight residual False -2.59 -0.80 -1.79 2.00e-01 2.50e+01 7.97e+01 chirality pdb=" CG LEU F 400 " pdb=" CB LEU F 400 " pdb=" CD1 LEU F 400 " pdb=" CD2 LEU F 400 " both_signs ideal model delta sigma weight residual False -2.59 -1.11 -1.48 2.00e-01 2.50e+01 5.46e+01 chirality pdb=" CG LEU C 153 " pdb=" CB LEU C 153 " pdb=" CD1 LEU C 153 " pdb=" CD2 LEU C 153 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 5863 not shown) Planarity restraints: 10969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 377 " 0.047 2.00e-02 2.50e+03 9.83e-02 1.45e+02 pdb=" CD GLN A 377 " -0.114 2.00e-02 2.50e+03 pdb=" OE1 GLN A 377 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN A 377 " 0.163 2.00e-02 2.50e+03 pdb="HE21 GLN A 377 " 0.036 2.00e-02 2.50e+03 pdb="HE22 GLN A 377 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 389 " 0.061 2.00e-02 2.50e+03 9.57e-02 1.37e+02 pdb=" CD GLN C 389 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN C 389 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN C 389 " -0.161 2.00e-02 2.50e+03 pdb="HE21 GLN C 389 " -0.030 2.00e-02 2.50e+03 pdb="HE22 GLN C 389 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 302 " 0.032 2.00e-02 2.50e+03 6.39e-02 4.08e+01 pdb=" C ASP F 302 " -0.111 2.00e-02 2.50e+03 pdb=" O ASP F 302 " 0.041 2.00e-02 2.50e+03 pdb=" N ILE F 303 " 0.038 2.00e-02 2.50e+03 ... (remaining 10966 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 6658 2.22 - 2.82: 161241 2.82 - 3.41: 193218 3.41 - 4.01: 243734 4.01 - 4.60: 383631 Nonbonded interactions: 988482 Sorted by model distance: nonbonded pdb=" O GLU D 557 " pdb=" H LYS D 572 " model vdw 1.630 2.450 nonbonded pdb=" O ASP C 694 " pdb=" HG1 THR C 697 " model vdw 1.641 2.450 nonbonded pdb=" H ALA E 914 " pdb=" O VAL E 936 " model vdw 1.651 2.450 nonbonded pdb=" O GLU A 352 " pdb="HH21 ARG A 358 " model vdw 1.655 2.450 nonbonded pdb=" O GLU B 557 " pdb=" H LYS B 572 " model vdw 1.663 2.450 ... (remaining 988477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 948)) selection = (chain 'B' and (resid 123 through 720 or (resid 721 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 t \ hrough 948)) selection = (chain 'C' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ selection = (chain 'D' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ selection = (chain 'E' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ selection = (chain 'F' and (resid 123 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 407 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or resid 408 through 411 or (resid 412 through 413 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or resid 414 through 720 or (resid 721 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH21 or name HH22)) or resid 722 through 948)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.960 Extract box with map and model: 2.170 Check model and map are aligned: 0.420 Set scattering table: 0.540 Process input model: 122.270 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.110 37777 Z= 0.749 Angle : 1.265 14.598 51044 Z= 0.694 Chirality : 0.071 1.785 5866 Planarity : 0.009 0.078 6545 Dihedral : 12.809 109.862 14528 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.48 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.12), residues: 4632 helix: -2.22 (0.08), residues: 2005 sheet: -3.86 (0.18), residues: 538 loop : 0.04 (0.15), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 770 HIS 0.036 0.003 HIS B 839 PHE 0.039 0.004 PHE A 547 TYR 0.054 0.004 TYR E 757 ARG 0.036 0.002 ARG B 652 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 4.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: -0.0097 (mtm) cc_final: -0.1522 (tmm) REVERT: C 334 MET cc_start: 0.5174 (mtt) cc_final: 0.4944 (ptp) REVERT: C 655 MET cc_start: 0.8886 (mmp) cc_final: 0.8637 (mmm) REVERT: C 826 MET cc_start: 0.8836 (tpp) cc_final: 0.8553 (tpp) REVERT: E 197 MET cc_start: -0.0894 (mmt) cc_final: -0.1117 (ptm) REVERT: F 197 MET cc_start: -0.2781 (mtp) cc_final: -0.3094 (mmt) REVERT: F 552 MET cc_start: 0.8383 (tpp) cc_final: 0.7987 (tpp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.9382 time to fit residues: 251.7548 Evaluate side-chains 146 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 4.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 20.0000 chunk 351 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 237 optimal weight: 20.0000 chunk 187 optimal weight: 0.9980 chunk 363 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 421 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN E 541 ASN E 715 GLN E 916 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37777 Z= 0.187 Angle : 0.631 10.998 51044 Z= 0.333 Chirality : 0.050 1.691 5866 Planarity : 0.005 0.058 6545 Dihedral : 6.485 113.704 5192 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.15 % Allowed : 5.23 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.12), residues: 4632 helix: -0.64 (0.10), residues: 2051 sheet: -3.57 (0.18), residues: 540 loop : -0.43 (0.15), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 464 HIS 0.007 0.001 HIS A 841 PHE 0.020 0.001 PHE A 547 TYR 0.017 0.001 TYR A 394 ARG 0.007 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 4.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: -0.0309 (mtm) cc_final: -0.1680 (ppp) REVERT: B 766 MET cc_start: 0.7914 (mmm) cc_final: 0.7605 (mmm) REVERT: B 810 MET cc_start: 0.8649 (mmp) cc_final: 0.8443 (tpp) REVERT: C 272 MET cc_start: 0.3845 (ttp) cc_final: 0.2028 (ptt) REVERT: C 334 MET cc_start: 0.5029 (mtt) cc_final: 0.4746 (ttp) REVERT: E 197 MET cc_start: -0.1155 (mmt) cc_final: -0.1356 (ptm) REVERT: F 197 MET cc_start: -0.2906 (mtp) cc_final: -0.3208 (mmt) outliers start: 6 outliers final: 3 residues processed: 153 average time/residue: 0.9277 time to fit residues: 240.7016 Evaluate side-chains 149 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain D residue 945 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 350 optimal weight: 7.9990 chunk 286 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 422 optimal weight: 7.9990 chunk 456 optimal weight: 2.9990 chunk 375 optimal weight: 0.4980 chunk 418 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 338 optimal weight: 3.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 376 GLN E 541 ASN E 715 GLN E 916 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 37777 Z= 0.277 Angle : 0.594 10.819 51044 Z= 0.312 Chirality : 0.050 1.711 5866 Planarity : 0.004 0.053 6545 Dihedral : 6.260 106.585 5192 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.37 % Allowed : 6.81 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.12), residues: 4632 helix: -0.05 (0.11), residues: 2058 sheet: -3.46 (0.19), residues: 541 loop : -0.71 (0.15), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 770 HIS 0.007 0.001 HIS B 839 PHE 0.020 0.001 PHE A 547 TYR 0.015 0.001 TYR C 544 ARG 0.004 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 4.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: -0.0209 (mtm) cc_final: -0.1630 (ppp) REVERT: B 766 MET cc_start: 0.8084 (mmm) cc_final: 0.7842 (mmm) REVERT: C 206 MET cc_start: -0.1397 (tpp) cc_final: -0.2966 (ttt) REVERT: C 272 MET cc_start: 0.3383 (ttp) cc_final: 0.1977 (ptt) REVERT: C 334 MET cc_start: 0.4747 (mtt) cc_final: 0.4478 (ttp) REVERT: C 576 CYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8784 (t) REVERT: C 810 MET cc_start: 0.8894 (pmm) cc_final: 0.8281 (pmm) REVERT: E 197 MET cc_start: -0.1116 (mmt) cc_final: -0.1392 (ptm) REVERT: F 197 MET cc_start: -0.2675 (mtp) cc_final: -0.3020 (mmt) REVERT: F 502 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8782 (mp) outliers start: 15 outliers final: 10 residues processed: 153 average time/residue: 0.8773 time to fit residues: 224.9208 Evaluate side-chains 156 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 4.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 945 ILE Chi-restraints excluded: chain E residue 682 CYS Chi-restraints excluded: chain F residue 502 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 4.9990 chunk 317 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 423 optimal weight: 8.9990 chunk 448 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 401 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 37777 Z= 0.349 Angle : 0.608 10.592 51044 Z= 0.321 Chirality : 0.050 1.677 5866 Planarity : 0.004 0.054 6545 Dihedral : 6.293 103.085 5192 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.54 % Allowed : 8.94 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.12), residues: 4632 helix: 0.05 (0.11), residues: 2066 sheet: -3.44 (0.19), residues: 546 loop : -1.00 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 464 HIS 0.006 0.001 HIS C 433 PHE 0.021 0.001 PHE A 547 TYR 0.016 0.001 TYR C 544 ARG 0.004 0.000 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: -0.0080 (mtm) cc_final: -0.1334 (ppp) REVERT: B 766 MET cc_start: 0.8113 (mmm) cc_final: 0.7863 (mmm) REVERT: C 206 MET cc_start: -0.1083 (tpp) cc_final: -0.2654 (ttt) REVERT: C 272 MET cc_start: 0.3957 (ttp) cc_final: 0.2602 (ptt) REVERT: C 334 MET cc_start: 0.4752 (mtt) cc_final: 0.4475 (ttp) REVERT: C 810 MET cc_start: 0.8899 (pmm) cc_final: 0.8485 (pmm) REVERT: E 197 MET cc_start: -0.0981 (mmt) cc_final: -0.1368 (ptm) REVERT: F 197 MET cc_start: -0.2744 (mtp) cc_final: -0.3047 (mmt) REVERT: F 502 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8771 (mp) REVERT: F 582 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8834 (t) REVERT: F 653 MET cc_start: 0.8826 (ptm) cc_final: 0.8373 (ptm) REVERT: F 655 MET cc_start: 0.8614 (mmm) cc_final: 0.8346 (mmm) outliers start: 22 outliers final: 12 residues processed: 160 average time/residue: 0.9166 time to fit residues: 250.0584 Evaluate side-chains 158 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 4.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 839 HIS Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 945 ILE Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 682 CYS Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 727 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 0.8980 chunk 254 optimal weight: 0.8980 chunk 6 optimal weight: 30.0000 chunk 333 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 382 optimal weight: 1.9990 chunk 310 optimal weight: 0.0870 chunk 0 optimal weight: 20.0000 chunk 229 optimal weight: 6.9990 chunk 402 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 37777 Z= 0.158 Angle : 0.523 10.543 51044 Z= 0.270 Chirality : 0.049 1.699 5866 Planarity : 0.003 0.052 6545 Dihedral : 5.909 101.722 5192 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.54 % Allowed : 8.91 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 4632 helix: 0.48 (0.11), residues: 2079 sheet: -3.20 (0.20), residues: 545 loop : -0.89 (0.15), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 464 HIS 0.008 0.001 HIS E 123 PHE 0.014 0.001 PHE E 820 TYR 0.014 0.001 TYR C 360 ARG 0.004 0.000 ARG C 563 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 4.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: -0.0152 (mtm) cc_final: -0.1419 (ppp) REVERT: B 766 MET cc_start: 0.8025 (mmm) cc_final: 0.7735 (mmm) REVERT: C 209 MET cc_start: -0.1573 (tpt) cc_final: -0.1785 (ttm) REVERT: C 272 MET cc_start: 0.4137 (ttp) cc_final: 0.2848 (ptt) REVERT: C 334 MET cc_start: 0.4650 (mtt) cc_final: 0.4343 (ttp) REVERT: C 576 CYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8801 (t) REVERT: C 733 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8690 (pm20) REVERT: E 197 MET cc_start: -0.1003 (mmt) cc_final: -0.1410 (ptm) REVERT: F 502 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8740 (mp) outliers start: 22 outliers final: 16 residues processed: 165 average time/residue: 0.9110 time to fit residues: 254.1204 Evaluate side-chains 164 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 4.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 839 HIS Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 945 ILE Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 682 CYS Chi-restraints excluded: chain E residue 826 MET Chi-restraints excluded: chain E residue 828 HIS Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 727 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 10.0000 chunk 403 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 263 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 448 optimal weight: 5.9990 chunk 372 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 622 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 37777 Z= 0.206 Angle : 0.524 10.485 51044 Z= 0.270 Chirality : 0.049 1.698 5866 Planarity : 0.003 0.049 6545 Dihedral : 5.833 98.152 5192 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.64 % Allowed : 9.43 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4632 helix: 0.67 (0.11), residues: 2079 sheet: -3.09 (0.20), residues: 540 loop : -0.93 (0.15), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 464 HIS 0.007 0.001 HIS E 622 PHE 0.015 0.001 PHE A 547 TYR 0.017 0.001 TYR C 360 ARG 0.003 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 4.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: -0.0236 (mtm) cc_final: -0.1460 (ppp) REVERT: B 766 MET cc_start: 0.8065 (mmm) cc_final: 0.7828 (mmm) REVERT: C 209 MET cc_start: -0.1551 (tpt) cc_final: -0.1761 (ttm) REVERT: C 272 MET cc_start: 0.4592 (ttp) cc_final: 0.3214 (ptt) REVERT: C 334 MET cc_start: 0.4465 (mtt) cc_final: 0.4152 (ttp) REVERT: C 576 CYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8817 (t) REVERT: C 733 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8922 (pm20) REVERT: C 810 MET cc_start: 0.8888 (pmm) cc_final: 0.8682 (pmm) REVERT: D 318 MET cc_start: -0.5629 (ptt) cc_final: -0.5882 (ptt) REVERT: E 197 MET cc_start: -0.0809 (mmt) cc_final: -0.1298 (ptm) REVERT: F 502 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8745 (mp) REVERT: F 582 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8790 (t) outliers start: 26 outliers final: 19 residues processed: 166 average time/residue: 0.8673 time to fit residues: 245.5700 Evaluate side-chains 169 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 839 HIS Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 945 ILE Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 682 CYS Chi-restraints excluded: chain E residue 738 THR Chi-restraints excluded: chain E residue 828 HIS Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 727 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 327 optimal weight: 20.0000 chunk 254 optimal weight: 0.9980 chunk 377 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 447 optimal weight: 8.9990 chunk 279 optimal weight: 4.9990 chunk 272 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 37777 Z= 0.243 Angle : 0.534 10.376 51044 Z= 0.276 Chirality : 0.049 1.694 5866 Planarity : 0.003 0.049 6545 Dihedral : 5.832 95.210 5192 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.74 % Allowed : 9.88 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4632 helix: 0.72 (0.11), residues: 2078 sheet: -3.08 (0.20), residues: 534 loop : -1.02 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 464 HIS 0.006 0.001 HIS B 839 PHE 0.017 0.001 PHE A 547 TYR 0.016 0.001 TYR C 360 ARG 0.006 0.000 ARG C 563 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 4.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: -0.0247 (mtm) cc_final: -0.1326 (ppp) REVERT: B 766 MET cc_start: 0.8082 (mmm) cc_final: 0.7841 (mmm) REVERT: C 272 MET cc_start: 0.4808 (ttp) cc_final: 0.3496 (ptt) REVERT: C 334 MET cc_start: 0.4466 (mtt) cc_final: 0.4149 (ttp) REVERT: C 576 CYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8828 (t) REVERT: E 197 MET cc_start: -0.0528 (mmt) cc_final: -0.1149 (ptm) REVERT: F 502 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8741 (mp) REVERT: F 582 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8754 (t) outliers start: 30 outliers final: 25 residues processed: 166 average time/residue: 0.9083 time to fit residues: 258.2490 Evaluate side-chains 170 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 945 ILE Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 682 CYS Chi-restraints excluded: chain E residue 738 THR Chi-restraints excluded: chain E residue 826 MET Chi-restraints excluded: chain E residue 828 HIS Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 727 ILE Chi-restraints excluded: chain F residue 842 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 267 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 284 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 221 optimal weight: 0.0040 chunk 41 optimal weight: 4.9990 chunk 351 optimal weight: 4.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 37777 Z= 0.227 Angle : 0.527 10.344 51044 Z= 0.271 Chirality : 0.049 1.694 5866 Planarity : 0.003 0.049 6545 Dihedral : 5.799 93.601 5192 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.89 % Allowed : 10.10 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4632 helix: 0.81 (0.11), residues: 2077 sheet: -3.02 (0.20), residues: 534 loop : -1.06 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 464 HIS 0.006 0.001 HIS B 839 PHE 0.016 0.001 PHE A 547 TYR 0.016 0.001 TYR C 360 ARG 0.003 0.000 ARG D 822 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 4.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.0333 (mtm) cc_final: -0.0954 (ppp) REVERT: B 766 MET cc_start: 0.8056 (mmm) cc_final: 0.7825 (mmm) REVERT: C 272 MET cc_start: 0.4848 (ttp) cc_final: 0.3583 (ptt) REVERT: C 334 MET cc_start: 0.4459 (mtt) cc_final: 0.4147 (ttp) REVERT: C 576 CYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8831 (t) REVERT: C 766 MET cc_start: 0.7944 (pmm) cc_final: 0.7561 (pmm) REVERT: E 197 MET cc_start: -0.0501 (mmt) cc_final: -0.1134 (ptm) REVERT: F 197 MET cc_start: -0.1448 (mmt) cc_final: -0.3198 (ttt) REVERT: F 502 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8739 (mp) REVERT: F 582 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8744 (t) outliers start: 36 outliers final: 29 residues processed: 172 average time/residue: 0.8857 time to fit residues: 261.8934 Evaluate side-chains 176 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 4.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 839 HIS Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 945 ILE Chi-restraints excluded: chain E residue 441 GLU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 682 CYS Chi-restraints excluded: chain E residue 738 THR Chi-restraints excluded: chain E residue 826 MET Chi-restraints excluded: chain E residue 828 HIS Chi-restraints excluded: chain E residue 942 ILE Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 727 ILE Chi-restraints excluded: chain F residue 842 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 20.0000 chunk 428 optimal weight: 5.9990 chunk 390 optimal weight: 8.9990 chunk 416 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 327 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 376 optimal weight: 5.9990 chunk 394 optimal weight: 20.0000 chunk 415 optimal weight: 0.0470 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 37777 Z= 0.344 Angle : 0.577 10.225 51044 Z= 0.300 Chirality : 0.049 1.682 5866 Planarity : 0.004 0.049 6545 Dihedral : 5.934 94.107 5192 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.94 % Allowed : 10.27 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 4632 helix: 0.64 (0.11), residues: 2081 sheet: -3.03 (0.21), residues: 532 loop : -1.22 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 464 HIS 0.007 0.001 HIS B 839 PHE 0.020 0.001 PHE A 547 TYR 0.016 0.001 TYR C 360 ARG 0.004 0.000 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 4.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.0601 (mtm) cc_final: -0.0727 (ppp) REVERT: B 766 MET cc_start: 0.8004 (mmm) cc_final: 0.7758 (mmm) REVERT: C 334 MET cc_start: 0.4098 (mtt) cc_final: 0.3749 (ttp) REVERT: C 766 MET cc_start: 0.8025 (pmm) cc_final: 0.7694 (pmm) REVERT: E 197 MET cc_start: -0.0462 (mmt) cc_final: -0.1112 (ptm) REVERT: F 502 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8741 (mp) outliers start: 38 outliers final: 32 residues processed: 174 average time/residue: 0.9367 time to fit residues: 280.9830 Evaluate side-chains 175 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 621 ASP Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 945 ILE Chi-restraints excluded: chain E residue 441 GLU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 682 CYS Chi-restraints excluded: chain E residue 738 THR Chi-restraints excluded: chain E residue 826 MET Chi-restraints excluded: chain E residue 828 HIS Chi-restraints excluded: chain E residue 942 ILE Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 727 ILE Chi-restraints excluded: chain F residue 842 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 4.9990 chunk 440 optimal weight: 5.9990 chunk 268 optimal weight: 0.1980 chunk 209 optimal weight: 0.7980 chunk 306 optimal weight: 3.9990 chunk 462 optimal weight: 30.0000 chunk 425 optimal weight: 0.9990 chunk 368 optimal weight: 0.0570 chunk 38 optimal weight: 4.9990 chunk 284 optimal weight: 0.5980 chunk 225 optimal weight: 0.0970 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 657 ASN E 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 37777 Z= 0.139 Angle : 0.511 10.327 51044 Z= 0.258 Chirality : 0.049 1.715 5866 Planarity : 0.003 0.047 6545 Dihedral : 5.597 94.908 5192 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.52 % Allowed : 10.67 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 4632 helix: 1.06 (0.12), residues: 2073 sheet: -2.85 (0.21), residues: 537 loop : -0.98 (0.15), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 464 HIS 0.006 0.001 HIS A 211 PHE 0.011 0.001 PHE F 455 TYR 0.015 0.001 TYR C 360 ARG 0.006 0.000 ARG C 563 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Residue THR 530 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 4.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.0538 (mtm) cc_final: -0.0704 (tmm) REVERT: B 766 MET cc_start: 0.7849 (mmm) cc_final: 0.7615 (mmm) REVERT: C 272 MET cc_start: 0.4255 (ttp) cc_final: 0.2594 (ptt) REVERT: C 334 MET cc_start: 0.3994 (mtt) cc_final: 0.3688 (ttp) REVERT: C 733 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8516 (pm20) REVERT: C 766 MET cc_start: 0.7967 (pmm) cc_final: 0.7596 (pmm) REVERT: E 197 MET cc_start: -0.0463 (mmt) cc_final: -0.1133 (ptm) REVERT: F 197 MET cc_start: -0.1378 (mmt) cc_final: -0.3140 (ttt) REVERT: F 502 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8737 (mp) outliers start: 21 outliers final: 18 residues processed: 164 average time/residue: 0.8758 time to fit residues: 245.2729 Evaluate side-chains 166 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 4.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain E residue 441 GLU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 682 CYS Chi-restraints excluded: chain E residue 826 MET Chi-restraints excluded: chain E residue 828 HIS Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 727 ILE Chi-restraints excluded: chain F residue 842 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 0.0980 chunk 392 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 chunk 339 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 368 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 378 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 67 optimal weight: 0.3980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 657 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.096845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.067176 restraints weight = 464656.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.069425 restraints weight = 203427.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.069713 restraints weight = 93602.891| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 37777 Z= 0.145 Angle : 0.498 10.316 51044 Z= 0.251 Chirality : 0.048 1.700 5866 Planarity : 0.003 0.048 6545 Dihedral : 5.480 91.765 5192 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.47 % Allowed : 10.86 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 4632 helix: 1.24 (0.12), residues: 2071 sheet: -2.80 (0.21), residues: 553 loop : -0.89 (0.15), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 464 HIS 0.006 0.001 HIS A 211 PHE 0.011 0.001 PHE A 547 TYR 0.015 0.001 TYR C 360 ARG 0.003 0.000 ARG C 705 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8151.06 seconds wall clock time: 142 minutes 11.55 seconds (8531.55 seconds total)